To identify overall and site-specific rates of nosocomial infections (NIs) during the neutropenic, as compared to the non-neutropenic stage of treatment in adult recipients of allogeneic and autologous bone marrow transplantation (BMT) and peripheral blood stem-cell transplantation (PBSCT), a prospective, 54-month study was started at the Haematological Stem Cell Transplantation Unit of the University Hospital of Freiburg, Germany. NI types were identified using modified CDC definitions. A total of 351 patients (14 256 in-patient days, 5026 neutropenic days) were investigated (316/90% allogeneic, 35/10% autologous; BMT: 119 patients, PBSCT: 234 patients). The mean length of neutropenia was 14.3 days (range: 0-66). Antimicrobial prophylaxis for allogeneic transplantation consisted of ciprofloxacin, trimethoprim/sulpha-methoxazole, fluconazole, and metronidazole. In total, 239 NIs were identified in 169 patients (48.1%), and of these 171 (71.5%) occurred during neutropenia (34.0 NIs per 1000 days at risk). The main pathogens were coagulase-negative staphylococci (36.3%), Clostridium difficile (20.4%), and enterococci (10.0%). Site-specific incidence densities during neutropenia vs non-neutropenia were: 13.9 vs 1.6 bloodstream infections (all central line-associated), 11.9 vs 1.8 pneumonias, 3.0 vs 2.9 gastroenteritis, and 1.6 vs 0.3 urinary tract infections. The greatest number of NI in BMT and PBSCT recipients is acquired during neutropenia, and multicentre surveillance programmes should focus on this.